Hi Sergei,

I am really hoping that you can help me.  I am running into issues saving a file in HyPhy.  I am running a very large local molecular clock analysis (on 122 sequences).

Here's how we run it...
Go to Standard Analyses
---Molecular Clock
---LocalMolClock.bf
---Click Nucleotide/Protein
----Enter the .fas file
----TRN
----Local
----Enter the vanilla newick tree.nwk file
----All Parameters

It processes for 1.5 hours on a quad-processor system.  Then, it's looking for input of more files to process.  There's never an opportunity to save the output (other than to cut and paste into notepad) for use elsewhere.
My goal is to save the analysis as a HYPHY file so that I can later access the data and use "object inspector" for further analyses (e.g. use "object inspector" to generate a tree using the molecular clock data).

Thanks, in advance, for your valuable input.